TATDN3

protein-coding

TatD DNase domain containing 3

Gene summary

Enables DNA-(apurinic or apyrimidinic site) endonuclease activity and single-stranded DNA 3'-5' DNA exonuclease activity. Predicted to be involved in DNA metabolic process. Located in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001042552.3

Inheritance

—

ClinVar variants

U:42B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr1:212,791,828-212,816,830

External References & Databases

Ensembl (ENSG00000203705)

Transcript & Mutation Effects

hg38 • Region Span ~25.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TATDN3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 35

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001042552.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			37 clinvar	3 clinvar		40
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	42	3	0	45

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 76 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001042552.3	RefSeq	NP_001036017.1	10	MANE Select
ENST00000366974.9	Ensembl	ENSP00000355941.4	10	MANE Select
NM_001042553.3	RefSeq	NP_001036018.1	10	Standard
NM_001146169.2	RefSeq	NP_001139641.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

nucleic acid phosphodiester bond hydrolysis

Molecular Function

nuclease activity
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000532324
Coding exons: 10
Length: 24799
Individuals with no LoFs: 125656
Homozygous LoFs: 1
Heterozygous LoFs: 90
Defined: 125747
p: 0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.432	130	145	0.899	0.00000697	1788
Missense (PolyPhen)		46	43.888	1.0481		530
Synonymous	0.435	49	53.0	0.924	0.00000242	554
Loss of Function	1.12	12	17.0	0.707	7.25e-7	219

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00087	0.00086	rare
Latino/Admixed American	0.00046	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00077	0.00076	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00029	0.00028	rare
South Asian	0.00049	0.00046	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative deoxyribonuclease.;

Intolerance Scores

LoFtool: 0.103
RVIS EVS: 1.15
RVIS percentile EVS: 92.47

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.494

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium